1,721,109 research outputs found
Reference data for isolated pyrrole
No full textThe dataset includes input and output files for the fitting of the rotational and vibrorotational transition lines related to the v=0,1,2 vibrational states of the NH out-of-plane bending motion of pyrrole in the gas phase using the SPFIT program of the CALPGM suite.
The following information is provided:
(i) fitting files for the normal species including pure rotational line transition of the ground and first excited vibrational state and vibrorotational bands of the fundamental, first overtone, and first hot band using the S-reduction and the Watson's III-l representation.
(ii) fitting files for the normal species including pure rotational line transition of the ground and first excited vibrational state and vibrorotational bands of the fundamental, first overtone, and first hot band using the Watson's S-reduction and the I-r representation.
(iii) fitting files for the rotational transition lines of the 13C2 isotopologue using the Watson's S-reduction and the III-l representation.
(iv) fitting files for the rotational transition lines of the 13C3 isotopologue using the Watson's S-reduction and the III-l representation
Reference data for Skaergaardite
No full textThe dataset includes numerical data from computational simulations carried out with Quantum ESPRESSO to characterize both the electronic and phonon dispersion bands and the density of states of Skaergaardite, a bimetallic compound of copper and palladium with formula CuPd and CsCl-like structure (B2).
The following information is provided:
(i) Crystal and energy structure
(ii) Electronic band structure
(iii) Electronic density of states
(iv) Projected electronic density of states
(v) Phonon band structure
(vi) Phonon density of states
(vii) Elastic and mechanical constant
Rotational spectroscopy signature of smelling allyl alcohols
No full textAllyl alcohol is a strong lachrymator with a pungent mustard odor. It is a fundamental building block
of several smelling organic molecules. Depending on the carbon frame, they present a quite different
odor, suggesting a modulation role of the molecular shape in the ligand-receptor interaction.
Rotational spectroscopy is a suitable tool to get insights on the structure of molecules and molecular
complexes in the gas phase and, in combination with computational chemistry simulations, allows
for exploration of high dimension conformational spaces. Here we present, for the first time, the rotational spectra and the analysis of three allyl alcohols: oct-1-en-3-ol (mushroom alcohol, C10H16O),
4,6,6-trimethylbicyclo[3.1.1]hept-3-en-2-ol (verbenol, C8H16O), and 3,7,11-trimethyl-2,6,10-dodecatrien-1-ol (farnesol, C15H26O).
The spectrum of oct-1-en-3-ol has been collected in the 59.6-74.4 GHz frequency range with the
free jet absorption millimeter wave spectrometer in Bologna. Two species were observed. In both of
them the allyl alcohol substructure is skew-gauche (referring to OCC=C and HOCC diehdral angles,
respectively) and the alkyl chain is all trans. The difference lies on the relative orientation of the alkyl
and allyl alcohol subunits.
The spectrum of cis-verbenol has been recorded in the 2-8 GHz frequency range with the chirpedpulse Fourier transform spectrometer in Valladolid. The rotational spectra of the parent, hydroxyl
deuterated, and all 13C-isotopologues have been assigned, allowing for structure’s determination.
Differently from solid state, in the gas phase the most stable conformer exhibits an anti HCOH arrangement. Observation of the 1:1 water complex has shown that water acts as proton donor to the
hydroxyl group, forming a secondary O-H interaction with alkyl verbenol’s hydrogen atoms.
With the same spectrometer, the spectrum of farnesol has been collected. Since farnesol is formed
by a mixture of 4 cis/trans-isomers, the spectrum is quite congested and, due to the presence of 8
rotatable bonds, the assignment is not straightforward. Preliminary considerations on the conformational space will be presented
Ring fluorination effects on molecular water clusters: the cases of 2-fluoropyridine, 3-fluoropyridine and penta-fluoropyridine. A rotational spectroscopy study.
No full textThe importance of organic fluorinated compounds in science and in everyday life is growing year after year.1 The effects of fluorination are related to the high electronegativity of this atom and its polarizability. In general the introduction of a fluorine atom is used in order to modulate physicochemical properties, like hydrophilicity and lipophilicity, of bio-organic molecules and functional materials.1,2 Additionally, structural changes can also be related to the electronic effect of the fluorine atom or to the molecule capability of creating new hydrogen bonds or non-covalent bonds, having fluorine as acceptor.
For this reason we investigate clusters where a molecule of water is used as a probe to reveal the changes on the electrostatic potential on the fluorinated compounds.
The experimental conditions are achieved in supersonic expansions using Molecular Beam Fourier Transform Microwave Spectroscopy technique (MBFTMW).3 The high resolution and sensitivity of rotational spectroscopy give direct access to the structural arrangement of the systems, allowing the measurement of bond lengths and angles. Moreover this gas phase technique allows unveiling subtle structural and dynamical effects usually related to changes in non-covalent interactions.
The series of clusters studied between different fluorinated pyridines and a molecule of water are: 2-fluoropyridine-water, 3-fluoropyridine-water and penta-fluoropyridine-water (see Figure 1) complexes. The results clearly show that the introduction of a single fluorine atom into a molecule already induces significant effects, but as the number of fluorine atoms increases, such as in the case of penta-fluoropyridine, the system starts to behave as a completely novel species.4 The perfluorination effect is clearly observable in the penta-fluoropyridine-water adduct where the water oxygen lone pairs point towards the aromatic ring.
Figure 1: the observed adducts of 2-fluoropyridine, 3-fluoropyridine and penta-fluoropyridine with a molecule of water
Reference data for isolated 2'-hydroxyacetophenone
No full textThe dataset includes numerical data from computational simulations on the four conformational isomers of 2'-hydroxyacetophenone (syn/syn, anti/syn, syn/anti, anti/anti) molecule carried out to determine their structure, relative energy and spectroscopic parameters. Moreover, the internal rotation barrier is also investigated for the global minimum (syn/syn). The following information is provided: (i) quantum mechanical calculations at the B3LYP-D3(BJ)/Def2-TZVP level for the four conformers of 2'-hydroxyacetophenone, (ii) quantum mechanical calculations at the MP2/aug-cc-pVTZ level for the most stable conformer of 2'-hydroxyacetophenone
Reference data for isolated 2'-aminoacetophenone and acetophenone
No full textThe dataset includes numerical data from computational simulations and free-jet absorption millimeter-wave spectroscopy measurements, carried out to determine the methyl internal rotation barrier of 2'-aminoacetophenone and acetophenone. The following information is provided: (i) quantum mechanical calculations at the MP2/aug-cc-pVTZ and the B3LYP-D3(BJ)/Def2-TZVP level for both the 2'-aminoacetophenone and acetophenone molecules (ii) input and output files for the fitting of the experimental rotational transition lines of 2'-aminoacetophenone performed with the XIAM code
Atropisomerism in bisphenols: free jet absorption millimeter wave study of 2,2’-biphenol
No full textThe rotational spectrum of 2,20-biphenol has been investigated by millimeter wave absorption free jet spectroscopy. The two sides of the phenyl rings with attached the hydroxyl group form a dihedral angle of 112.78. Each hydroxyl group is nearly co-planar to the ring to which it belongs, and points towards the p system of the adjacent ring
Density Functional Theory Simulations of Skaergaardite (CuPd) with a Self-Consistent Hubbard U-Correction
Full text linkThe electronic and phonon bands of Skaergaardite are investigated using density functional theory (DFT) as implemented in Quantum ESPRESSO. Skaergaardite is a copper palladium mineral (CuPd) found in the Skaergaard intrusion with a CsCl-type (B2) structure. Due to its porous structure, it presents a large surface area available for interactions, which makes it a promising catalyst. The PBE-GGA functional with a Hubbard-like localized term (DFT+U) is combined with ultrasoft and norm-conserving pseudopotentials, and a conventional approach with a dense Monkhorst–Pack grid of k-points 12×12×12 is applied. The electronic valence bands are mainly constituted by 3d orbitals of Cu and 4d orbitals of Pd and a pseudo-gap can be recognized. With respect to DFT, DFT+U causes a general downward shift in the valence band. The acoustic and optical phonon branches are separated by a few cm−1 gap at about 150 cm−1 and show a density of state curve typical of ordered materials. These results highlight the reliability of DFT+U in studying bimetallic systems with scarce experimental benchmarks, offering insights into the behavior of Skaergaardite and its potential applications in material science such as reduction reactions and hydrogen storage
Conformational preferences of molecules, biomolecules and molecular complexes: the importance of the hydrogen bond and other non-bonding interactions
No full textRotational spectroscopy of non-covalently bound complexes of medium size organic molecules
Full text linkThe conformational space of non-covalently bound complexes of medium size organic molecules is shaped by competing interactions occurring within the molecules or with the partners. It usually presents a high number of low energy conformations very close in energy with shallow potential energy barriers through which the molecular system can tunnel.
The conformational preferences of non-covalently bound complexes can be studied to a very high degree of accuracy by free jet rotational spectroscopy1 and from the detailed structural and dynamical data that can be obtained, the site and geometry of the interaction and information on the binding energy can be inferred without ambiguity.
The questions usually addressed are: which is the preferred binding site, which type of interactions are established, and whether any conformational change takes place in the monomers upon complexation. Answers to these questions allow insight into the molecular interaction process at the molecular level, bridging the gap between gas-phase and bulk properties.
Chosen examples of published and unpublished results of complexes of medium-size organic molecules with different partners formed in a supersonic expansion and characterized by rotational spectroscopy will be discussed. The partner molecules are held together by hydrogen bonds, weak hydrogen bonds and lone-pair--hole interactions.
It will be shown how non-bonding interactions compete to shape the conformational space of the complexes, the structural changes brought to the conformers of the monomers by complexation and how these interactions can be drastically changed through atomic or functional group substitution
- …
